Polk LSI 25's say set to Large

I have read all of the info on this site and you say to set all speakers to small and let the sub do the work. My manual for my LSI 25's say "set to Large" because they have their own sub. What to do? Audyssey sets them to Large (I have an Onkyo tx-806) when I run it. The LSi 25's have two hookups in the back. the top for the speakers and the bottom for the subwoofer in them. What to you think is best? By the way, I have a powerful sub in the Polk PSW650.

Should I remove the jumpers between the two hookups in the back of my tower speakers? I would then set my towers to "Small" set the crossover to 80 and let the sub do the work. Right? Also, I have my AVR subwoofer out going into my subs LFE in. You mentioned the line input on my sub. Any difference?

I recommend using y-cords to split the subwoofer out of your AVR to the Sub In RCA connections on the speakers (yes, remove the jumpers) and also to the separate sub. You will need two y-cords to split the signal into three paths. The LFE in is the best one to use for the sub. More info on subs and MultEQ here:

I guess my real question is this: Do I need the towers subs? Should I only use the subwoofer or will I be missing needed bass if I bypass the towers subs? If I leave it as I have it (with the subs on the towers connected with the jumper but the crossover set at 80) isn't all of the bass going to the subwoofer anyhow?

There are advantages in reproducing the bass from multiple subs. Room modes are driven from more points and thus overlap more to give a smoother response. Furthermore, MultEQ and MultEQ XT create higher resolution filters in the subwoofer channel as compared to the satellite channels. So, by using the woofers as subs you are taking advantage of this higher resolution.

So I will leave the jumpers in (if I decide not to do the y-cords) and let Audyssey run its program. When my AVR sets the towers to Full Band (which it always does) I will change it back to small and 80 crossover and I will still then have 3 subs working but not as well as the y-cords will give me. Correct?

Nope... If you don't connect the subs to the Sub Out then they are not "Subs". They are just woofers for your front L and R speakers. To make them Subs you have to feed them the bass managed signal that comes out of the Sub Out connector on the AVR.